Chaste Release::3.1
NodeBasedCellPopulationWithParticles< DIM > Member List
This is the complete list of members for NodeBasedCellPopulationWithParticles< DIM >, including all inherited members.
AbstractCellPopulation(AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
AbstractCellPopulation(AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
AbstractCentreBasedCellPopulation(AbstractMesh< ELEMENT_DIM, ELEMENT_DIM > &rMesh)AbstractCentreBasedCellPopulation< DIM > [protected]
AbstractCentreBasedCellPopulation(AbstractMesh< ELEMENT_DIM, ELEMENT_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())AbstractCentreBasedCellPopulation< DIM >
AbstractOffLatticeCellPopulation(AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM > [protected]
AbstractOffLatticeCellPopulation(AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM >
AddCell(CellPtr pNewCell, const c_vector< double, DIM > &rCellDivisionVector, CellPtr pParentCell)NodeBasedCellPopulationWithParticles< DIM > [virtual]
AbstractCentreBasedCellPopulation< DIM >::AddCell(CellPtr pNewCell, const c_vector< double, ELEMENT_DIM > &rCellDivisionVector, CellPtr pParentCell=CellPtr())AbstractCentreBasedCellPopulation< DIM >
AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::AddCell(CellPtr pNewCell, const c_vector< double, SPACE_DIM > &rCellDivisionVector, CellPtr pParentCell=CellPtr())=0AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [pure virtual]
AddCellUsingLocationIndex(unsigned index, CellPtr pCell)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [virtual]
AbstractCentreBasedCellPopulation< DIM >::AddNode(Node< SPACE_DIM > *pNewNode)=0AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM > [pure virtual]
Begin()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
boost::serialization::access classNodeBasedCellPopulationWithParticles< DIM > [friend]
Clear()NodeBasedCellPopulation< DIM >
CloseOutputFiles()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [virtual]
CreateCellPair(CellPtr pCell1, CellPtr pCell2)AbstractCentreBasedCellPopulation< DIM >
CreateOutputFiles(const std::string &rDirectory, bool cleanOutputDirectory)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [virtual]
End()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
GenerateCellResults(CellPtr pCell, std::vector< unsigned > &rCellProliferativeTypeCounter, std::vector< unsigned > &rCellCyclePhaseCounter)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [virtual]
GenerateCellResultsAndWriteToFiles()AbstractCentreBasedCellPopulation< DIM > [virtual]
GetAbsoluteMovementThreshold()AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM >
GetBoxCollection()NodeBasedCellPopulation< DIM >
GetCellAncestors()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
GetCellMutationStateCount()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
GetCellPropertyRegistry()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
GetCellsUsingLocationIndex(unsigned index)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
GetCellUsingLocationIndex(unsigned index)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
GetCentroidOfCellPopulation()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
GetDampingConstant(unsigned nodeIndex)AbstractCentreBasedCellPopulation< DIM > [virtual]
GetDampingConstantMutant()AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM >
GetDampingConstantNormal()AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM >
GetIdentifier() const Identifiable
GetLocationIndexUsingCell(CellPtr pCell)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
GetLocationOfCellCentre(CellPtr pCell)AbstractCentreBasedCellPopulation< DIM > [virtual]
GetMechanicsCutOffLength()NodeBasedCellPopulation< DIM >
GetMeinekeDivisionSeparation()AbstractCentreBasedCellPopulation< DIM >
GetNeighbouringNodeIndices(unsigned index)NodeBasedCellPopulation< DIM > [virtual]
GetNode(unsigned index)NodeBasedCellPopulation< DIM > [virtual]
GetNodeCorrespondingToCell(CellPtr pCell)AbstractCentreBasedCellPopulation< DIM >
GetNumNodes()NodeBasedCellPopulation< DIM > [virtual]
GetNumRealCells()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
GetOutputCellAges()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
GetOutputCellAncestors()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
GetOutputCellCyclePhases()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
GetOutputCellIdData()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
GetOutputCellMutationStates()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
GetOutputCellProliferativeTypes()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
GetOutputCellVariables()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
GetOutputCellVolumes()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
GetParticleIndices()NodeBasedCellPopulationWithParticles< DIM >
GetSizeOfCellPopulation()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
GetUseVariableRadii()NodeBasedCellPopulation< DIM >
GetVolumeOfCell(CellPtr pCell)NodeBasedCellPopulation< DIM > [virtual]
GetWidth(const unsigned &rDimension)NodeBasedCellPopulation< DIM > [virtual]
InitialiseCells()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
IsCellAssociatedWithADeletedLocation(CellPtr pCell)AbstractCentreBasedCellPopulation< DIM > [virtual]
IsCellAttachedToLocationIndex(unsigned index)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
IsGhostNode(unsigned index)AbstractCentreBasedCellPopulation< DIM > [virtual]
IsMarkedSpring(const std::pair< CellPtr, CellPtr > &rCellPair)AbstractCentreBasedCellPopulation< DIM >
IsParticle(unsigned index)NodeBasedCellPopulationWithParticles< DIM > [virtual]
mAbsoluteMovementThresholdAbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM > [protected]
MarkSpring(std::pair< CellPtr, CellPtr > &rCellPair)AbstractCentreBasedCellPopulation< DIM >
mCellCyclePhaseCountAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mCellLocationMapAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mCellProliferativeTypeCountAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mCellsAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mCentroidAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mDampingConstantMutantAbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM > [protected]
mDampingConstantNormalAbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM > [protected]
mDirPathAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mIsParticleNodeBasedCellPopulationWithParticles< DIM > [private]
mLocationCellMapAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mMarkedSpringsAbstractCentreBasedCellPopulation< DIM > [protected]
mMeinekeDivisionSeparationAbstractCentreBasedCellPopulation< DIM > [protected]
mOutputCellAgesAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mOutputCellAncestorsAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mOutputCellCyclePhasesAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mOutputCellIdDataAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mOutputCellMutationStatesAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mOutputCellProliferativeTypesAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mOutputCellVariablesAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mOutputCellVolumesAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
MoveCellInLocationMap(CellPtr pCell, unsigned old_index, unsigned new_index)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
mpCellAgesFileAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mpCellCyclePhasesFileAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mpCellIdFileAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mpCellMutationStatesFileAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mpCellProliferativeTypesFileAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mpCellPropertyRegistryAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mpCellVariablesFileAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mpCellVolumesFileAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mpVizBoundaryNodesFileAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mpVizCellAncestorsFileAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mpVizCellProliferativePhasesFileAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mpVizCellProliferativeTypesFileAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mpVizNodesFileAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mpVtkMetaFileAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
mrMeshAbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [protected]
NodeBasedCellPopulation(NodesOnlyMesh< DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false, bool validate=true)NodeBasedCellPopulation< DIM >
NodeBasedCellPopulation(NodesOnlyMesh< DIM > &rMesh)NodeBasedCellPopulation< DIM >
NodeBasedCellPopulationWithParticles(NodesOnlyMesh< DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false)NodeBasedCellPopulationWithParticles< DIM >
NodeBasedCellPopulationWithParticles(NodesOnlyMesh< DIM > &rMesh)NodeBasedCellPopulationWithParticles< DIM >
OutputCellPopulationInfo(out_stream &rParamsFile)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
OutputCellPopulationParameters(out_stream &rParamsFile)NodeBasedCellPopulationWithParticles< DIM > [virtual]
RemoveCellUsingLocationIndex(unsigned index, CellPtr pCell)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [virtual]
RemoveDeadCells()NodeBasedCellPopulation< DIM > [virtual]
rGetCellCyclePhaseCount() const AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
rGetCellProliferativeTypeCount() const AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
rGetCells()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
rGetMesh()NodeBasedCellPopulation< DIM >
rGetMesh() const NodeBasedCellPopulation< DIM >
rGetNodePairs()NodeBasedCellPopulation< DIM > [virtual]
rGetParticles()NodeBasedCellPopulationWithParticles< DIM >
serialize(Archive &archive, const unsigned int version)NodeBasedCellPopulationWithParticles< DIM > [inline, private]
SetAbsoluteMovementThreshold(double absoluteMovementThreshold)AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM >
SetCellAncestorsToLocationIndices()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
SetCellUsingLocationIndex(unsigned index, CellPtr pCell)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
SetDampingConstantMutant(double dampingConstantMutant)AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM >
SetDampingConstantNormal(double dampingConstantNormal)AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM >
SetDataOnAllCells(const std::string &dataName, double dataValue)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
SetDefaultMutationStateOrdering()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
SetMechanicsCutOffLength(double mechanicsCutOffLength)NodeBasedCellPopulation< DIM >
SetMeinekeDivisionSeparation(double divisionSeparation)AbstractCentreBasedCellPopulation< DIM >
SetNode(unsigned nodeIndex, ChastePoint< DIM > &rNewLocation)NodeBasedCellPopulation< DIM >
AbstractCentreBasedCellPopulation< DIM >::SetNode(unsigned nodeIndex, ChastePoint< SPACE_DIM > &rNewLocation)=0AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM > [pure virtual]
SetOutputCellAges(bool outputCellAges)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
SetOutputCellAncestors(bool outputCellAncestors)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
SetOutputCellCyclePhases(bool outputCellCyclePhases)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
SetOutputCellIdData(bool outputCellIdData)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
SetOutputCellMutationStates(bool outputCellMutationStates)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
SetOutputCellProliferativeTypes(bool outputCellProliferativeTypes)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
SetOutputCellVariables(bool outputCellVariables)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
SetOutputCellVolumes(bool outputCellVolumes)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
SetParticles(const std::set< unsigned > &rParticleIndices)NodeBasedCellPopulationWithParticles< DIM > [private]
SetUseVariableRadii(bool useVariableRadii=true)NodeBasedCellPopulation< DIM >
TestNodeBasedCellPopulationWithParticles (defined in NodeBasedCellPopulationWithParticles< DIM >)NodeBasedCellPopulationWithParticles< DIM > [friend]
UnmarkSpring(std::pair< CellPtr, CellPtr > &rCellPair)AbstractCentreBasedCellPopulation< DIM >
Update(bool hasHadBirthsOrDeaths=true)NodeBasedCellPopulation< DIM > [virtual]
UpdateNodeLocations(const std::vector< c_vector< double, DIM > > &rNodeForces, double dt)NodeBasedCellPopulationWithParticles< DIM >
NodeBasedCellPopulation::UpdateNodeLocations(const std::vector< c_vector< double, ELEMENT_DIM > > &rNodeForces, double dt)AbstractCentreBasedCellPopulation< DIM > [virtual]
AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::UpdateNodeLocations(const std::vector< c_vector< double, SPACE_DIM > > &rNodeForces, double dt)=0AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM > [pure virtual]
UpdateParticlePositions(const std::vector< c_vector< double, DIM > > &rNodeForces, double dt)NodeBasedCellPopulationWithParticles< DIM >
UpdateParticlesAfterReMesh(NodeMap &rMap)NodeBasedCellPopulationWithParticles< DIM > [virtual]
Validate()NodeBasedCellPopulationWithParticles< DIM > [protected, virtual]
WriteCellIdDataToFile()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
WriteCellResultsToFiles(std::vector< unsigned > &rCellProliferativeTypeCounter, std::vector< unsigned > &rCellCyclePhaseCounter)AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >
WriteResultsToFiles()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [virtual]
WriteTimeAndNodeResultsToFiles()AbstractCentreBasedCellPopulation< DIM > [virtual]
WriteVtkResultsToFile()NodeBasedCellPopulationWithParticles< DIM > [virtual]
~AbstractCellPopulation()AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > [virtual]
~Identifiable()Identifiable [virtual]
~NodeBasedCellPopulation()NodeBasedCellPopulation< DIM > [virtual]